Mercurial > repos > iuc > mothur_split_groups

annotate split.groups.xml @ 4:7b20827f8e8f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
author iuc
date Tue, 20 Mar 2018 14:14:32 -0400
parents 883a95e17395
children
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1 <tool profile="16.07" id="mothur_split_groups" name="Split.groups" version="@WRAPPER_VERSION@.0">
089c0f0c6c18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Generates a fasta file for each group</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @SHELL_OPTIONS@
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11
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12 ## create symlinks to input datasets
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13 ln -s '$name' name.dat &&
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14 ln -s '$count' count.dat &&
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15 ln -s '$fasta' fasta.dat &&
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16 ln -s '$group' group.dat &&
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17
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18 echo 'split.groups(
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19 #if $name:
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20 name=name.dat,
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21 #end if
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22 #if $groups:
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23 groups=${ str($groups).replace(",","-") },
883a95e17395 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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24 #end if
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25 #if $count:
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26 count=count.dat,
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27 #end if
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28 fasta=fasta.dat,
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29 group=group.dat
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30 )'
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31 | sed 's/ //g' ## mothur trips over whitespace
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32 | mothur
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33 | tee mothur.out.log
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34 ]]></command>
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35 <inputs>
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36 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/>
089c0f0c6c18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 <param name="name" type="data" format="mothur.names" label="name - Names to split by group" optional="true"/>
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38 <param name="group" type="data" format="mothur.groups" label="group - Groups"/>
089c0f0c6c18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
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40 <options>
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41 <filter type="data_meta" ref="group" key="groups"/>
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42 </options>
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43 </param>
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44 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
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45 <expand macro="param-savelog"/>
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46 </inputs>
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47 <outputs>
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48 <expand macro="logfile-output"/>
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49 <collection name="groupfastas" type="list" label="${tool.name} on ${on_string}: fasta per group">
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50 <!-- TODO: format_source on discovered collection elements doesn't seem to work yet, change to format_source="fasta" once it does -->
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51 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
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52 </collection>
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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57 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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58 <output_collection name="groupfastas" count="2">
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59 <element name="pasture" md5="3844bc02ec09acbbf31845ea6ac6632d" ftype="fasta"/>
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60 <element name="forest" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/>
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61 </output_collection>
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62 <param name="savelog" value="true"/>
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63 <expand macro="logfile-test"/>
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64 </test>
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65 </tests>
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66 <help><![CDATA[
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67
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68 @MOTHUR_OVERVIEW@
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69
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70 **Command Documentation**
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71
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72 The split.groups_ command reads a fasta file and group_ file and generates a fasta file for each group in the groupfile. A name_ file can also be split into groups.
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73
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74 .. _group: https://www.mothur.org/wiki/Group_file
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75 .. _name: https://www.mothur.org/wiki/Name_file
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76 .. _split.groups: https://www.mothur.org/wiki/Split.groups
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78 ]]></help>
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79 <expand macro="citations"/>
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80 </tool>